Ninja of Tokyo3
by zerohour20xx
Summary: Naruto is sent to another world due to Madara using a dimension technique. Narutoxharem Discontinued. Check out the remake: A Second Age
1. Chapter 1

From Shinobi to Eva Pilot

Original: 2241 words

Rewrite: 4578 words

A/N (4/22/2010): Well here is the rewrite of chapter one. Naruto will not be using many jutsu in the early chapters but in the later ones I have not decided yet. This story was an idea from Challenger. It will be a harem but it won't be a smut fest. I personally think that sometimes a lemon can hurt a story and too many can utterly ruin a story. *cough* Kyuubi16 *cough*. You may notice that some of the characters personalities will be OOC at times but they will be mostly the same at the core. Original material that belongs to me will be in bold at the end of the chapter. If you want to use them then ask first and give me credit in your story.

Note to Evangelion fans: This story will be different from the original plot because, for one, I hated the ending even though is was good in some points. With Naruto replacing Shinji, he will not have that, in my opinion, spineless nature where he will constantly apologize or try to run away. It will have some things and ideas from the Evangelion Rebuild: You are (not) alone, the Evangelion manga, and Evangelion Gakuen Datenroku.

Note to Challenger: This is a mix of the original version, the new version, and some of my own ideas.

Narutoxharem, slight Gendo bashing, slight Kaji bashing, gore, violence, language, possible sexual themes.

Those that have read this story before will need to reread it as it went under vast changes. That is to be expected when you double the original length.

Disclaimer: I don't own Naruto or Neon Genesis Evangelion.

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The destroyed Valley of the End was the battlefield of Madara Uchiha and Naruto Uzumaki-Namikaze. The world had been devastated by the Akatsuki but even they were just pawns to Madara. By using the power of eight of the nine Bijuu, he enacted his plan to wipe out all human life on the planet other than himself and a woman that he had under the control of his Eternal Mangekyo Sharingan to rebuild the world with him as the eternal ruler but his plan had a single flaw...Naruto still lived thanks the Kyuubi sealed inside him.

A battle scarred Naruto glared at Madara with a single vivid blue eye, his other red and looking blurred and dull. His once bright blonde hair was now covered in blood, whose blood it was was unknown to Naruto. "Madara, you have killed every single person that I have ever cared about. I will not allow you to live any longer." Naruto said as a Rasengan appeared in the palm of his hand.

The torso and head of Madara simply laughed. "You fool, you truly believe that you've won..." His eyes become pure black and the area in front of him was ripped open. "Have fun in the eternal rift." Madara laughed as Naruto was sucked into the rip in time and space.

Naruto felt like his limbs were being ripped from his torso as he was pulled farther into black void and he tried to get his bearings but was unable to as his body spun continuously. He felt a pull from inside himself and saw that he was in his mindscape. "Hey Kyuubi, do you have any idea where we are?" Naruto asked.

The giant nine-tailed fox shifted into his human appearance. (Looks like Naruto but with dark red hair.) "Well kit, Madara sent us to an Empty Rift, which is known as a realm between worlds. We can't go back to our world because of the force that ripped time and space to send us here but if your lucky, which you always are, you can go to a new world." Kyuubi said with a sigh.

"If I'm lucky? Don't you mean if we're lucky?" Naruto said with his head in confusion. Kyuubi looked at Naruto with a sad smile. "The only reason that your even alive is because my youkai reacted to your regenerative kekkei genkai. The only way for you to live the second jump is if I give you the rest of my youkai and turn you into a hanyou. I have lived many millenia but never have I seen a soul more deserving of a second chance at life. Good-bye, Naruto Uzumaki-Namikaze." Kyuubi said as his body turned into a small ethereal fox and entered Naruto. When the fox entered Naruto completely, the youkai of the Kyuubi began to mix with Naruto and a second hole opened up and he was thrown into the portal. As he came closer to the end of the portal, he began to reverse in age until her was a baby no older than 6 months old.

[Tokyo-3 park]

It was early Sunday morning and a dark auburn haired woman in her mid-twenties sat and looked out towards the river from the bench that she sat on, her name was Yui Ikari. She was relaxing after a long week working for Gehirn and had been upset after just finding out that Gendo was infertile and was unable to give her child. For all of her knowledge and work as a scientist, the one thing that she truly wanted to be was a mother. She wanted to raise a child and watch it grow up into an adult and then have children of its own. When she had originally talked to Gendo about children, he had been very forward about the name if they had a son, Shinji. Yui didn't really like the name but she had wanted Rei if they had a daughter. Of course this was back when she thought that Gendo could still give her a child

As her frustration neared a max when she heard what sounded like a baby crying. She followed the crying into the shrubs near where she was sitting and say a baby not even a year old with blonde hair and blue eyes with three marks on each of his cheeks. "And who are you little one?" she wondered aloud until she saw something catch her eye."You have such a beautiful necklace and...a locket?" she said in slight surprise as she moved the green crystal necklace aside and saw a small locket with the image of a nine-tailed fox on the front of it. She turned it to the other side and saw something etched into the metal. "Naruto, is that your name, little one? Well Naruto, it seems as though fate wishes for us to meet. I don't know why someone would leave you out here alone but I won't let you be harmed by someone's negligence. Don't worry, your new okaa-san will never leave you." Yui said with a smile on her face as she picked up Naruto and took him from the park.

Yui brought Naruto back to her home and saw that Gendo was home. Gendo Ikari was a man in his late twenties dark brown hair and his eyes covered by his sun glasses. When he saw the child, he immediately frowned. Yui saw this and knew that she was not going to let Gendo have his way this time.

[Three years later]

It had been three years since Yui had brought little Naruto back to her and Gendo's home. Gendo had originally been totally against having anything to do with the child and had even demanded that Yui take Naruto back to where ever she had found him but this had brought Yui's maternal fury at the mere mention of it and she had torn into Gendo and verbally ripped him to piece until he agreed with her.

Those three years had been hard for Naruto since he would have these nightly dreams of a boy that seemed so familiar to him and he would see everything that had happened. The beatings from drunks, the scorn and hatred from the other people in the dreams, and the inner-strength that the boy seemed to have in how he always smiled and proclaimed that he would become Hokage someday...whatever that was. In one of his dreams, he was able to hear a woman's voice calling him "son" but it wasn't Yui's voice, he had no idea what it meant.

Today was the first test of Gehirn's robot and Yui was currently in the pilot seat. She knew that Naruto was watching and was wondering what he thought of what she had helped create. The tests were going perfectly until the robot started to move on its own and act erratic. With a single roar the robot stopped but Yui was no longer in the pilot seat, only her plugsuit remained. Naruto had looked on totally frozen throughout the entire ordeal.

Three months later, Naruto was sitting on the floor in the Ikari home all alone. 'Kaa-san, you told me that you would never leave me but now you aren't here.' Naruto thought to himself as he finally accepted that Yui, his mother, would probably never return and tears started to flow from his eyes. He hadn't heard from Gendo, his adopted father, for the past month. He had to do everything himself cooking to cleaning. It had reminded him of his dreams of that boy in the orange jumpsuit, the young orphan that had to do everything for himself because no one cared enough to help.

Naruto turned around as he heard the door open and rushed to Gendo to hug him after not seeing the man in so long only to be stopped by a hand on his head. "Naruto, I'm leaving. Your a man, you don't need me. Good-bye." With that Gendo walked back out the door for the final time. A few minutes later, Naruto was still in shock. "He's left...just like kaa-san. Why...why is this happening to me!" Naruto yelled out as a red glow covered his body. As the red glow spread to his entire body, images began to flash in his mind to the point that he held his head tightly in pain.

He saw the boy that he had been in his dreams and something just clicked in his mind. The boy that he had seen in his dreams for so long was actually himself but he had no idea how it could be. With the sudden revelation, Naruto fell into unconsciousness.

Naruto looked around as he woke up. He was no longer in the Ikari home but in appeared to be a sewer, and a very familiar one at that. "I remember this place from my dreams. Were those actually my memories?" he said to himself but froze as he heard a chuckle. "It has been a few years hasn't it, kit?" said the deep, familiar voice. Naruto looked around for the source of the voice and then a figure appeared right in front of him and he fell backwards in surprise.

Naruto looked up and saw another person from his dreams. "K-Kyuubi? So...those weren't just dreams then?" Naruto asked figure in front of him but upon further attention to the looks of the person he noticed that he had an almost ghostly appearance and transparency. The man was wearing a dark red kimono and had long, blood-red hair. "Heh, it seems like you lost a lot of your memories but that's probably for the best. I cannot stay here for very long since Kami has only granted me this small favor in order to fix some of your memories." Kyuubi said as he pressed a glowing finger to Naruto's forehead. No other memories came back when this happened but what Naruto did see was the ability to use chakra like he had in his past life as well as a few jutsu that he had known. When Naruto broke out of his trance, he saw that Kyuubi was smiling. "Good luck in this world, Kit. Know that everyone is watching down on you, cheering you on." Kyuubi said as he slowly disappeared. "I will make everyone proud of me, Kyuubi. That is a promise of a lifetime." Naruto said with a fire in his eyes as he disappear from his mindscape.

[11 years later]

Over the next eleven years, Naruto trained in the ways of the ninja once again but he also learn what he could from libraries by using the Kage bushin no jutsu. He still went to school because he wanted to learn somethings on his own. At age ten, a jutsu that he had created back in his life appeared in his mind: Chi bushin no jutsu. The Chi bushin was an advanced version of the Kage bushin and lasted much longer and was more organized since it was a more complete copy. Naruto started to use his Kage bushins to work at part-time jobs and had his Chi bushins under henge's do harder work with one in college working towards a Bachelor's degree while he himself went to a normal school at a normal grade for his age.

Naruto had gotten an apartment later that year and had gotten used to the life that he was now living. Over the next three years, Naruto had come to terms with the fact that he may never remember his full life as he could only fully remember his life up to his tenth birthday back in his old world and the rest were just random flashes of information. He had finally gotten a Bachelor's degree in technological science and bio-chemistry after working all those years. He may have been very intelligent in those fields but he wasn't a "super genius".

Naruto walked into his apartment wearing a pair of black uniform pants and a white, button-up shirt. He noticed that there was a something in his mailbox. It looked like just a simple envelope so he took it inside. "Who the hell could this be from? NERV? Isn't that what Gehirn became? Lets see..." Naruto said and grabbed a kunai that he had made at one of the few remaining blacksmiths and opened the envelop and found that there was some sort of ID, a letter, and a postcard . He read the letter first and was angered by its contents. "That arrogant bastard. Why does he want to see me after eleven years?" Naruto wondered before an evil smirk graced his lips. "Oh, I'll go see him. Maybe I can make his life hell." Naruto said with a mischievous chuckle as he walked into his bedroom to pack his bags. He grabbed the postcard and the ID and put it into his back pocket and sent in the payment for his apartment for the next two years since he didn't know how long he would be gone. He had packed his normal clothes normally but he put everything else into scrolls and put the scrolls into seals on his belt. "I guess its time to face the past." He said as he closed the door behind him and left for Tokyo-3.

[6 hours later]

Naruto got off the train. He had changed on the empty train was now wearing a short sleeved orange T-shirt and black pants similar to the ones he used to wear back home. He looked around and saw that the streets were empty. "Why is the city so empty?" He said and pulled out the postcard. l He saw that it was a picture of a very hot woman and had some writing on it. 'To Naruto, I'm going to pick you so please wait for me! PS: Note the cleavage!' "The damn train had to stop two stations from where I'm suppose to be so I guess I'm walking." he said with a sigh.

He starts walking down the road until he sees three jets fly not very far above him and seconds later, a cruise missile from each zoomed about six feet above his head. He used his chakra to keep himself from falling due to the sonic boom caused by the missiles and turns around to see where the jets were heading and saw a large monster behind him a mile or so away. "Damn, that things big. But what is it?" He says. He sees a car coming straight for him but stops just next to him. "Sorry to keep you waiting, Naruto. C'mon, get in." said the woman in the car. It was the woman from the picture. "Katsuragi-san, right?" he asks as he hops into the passenger seat. "So what the hell was that thing?" Naruto asks as he points back to the monster. "We call that thing an Angel. And call me Misato, Katsuragi-san makes me sound like an old woman." she says with a laugh as she puts her foot on the gas and causes Naruto to hit the dashboard in front of him. "At least wait until I have the seatbelt on, geez." he grumbled.

The trip had been uneventful other than the high speeds but that was until they saw the JSSDF helicopters fly overhead with something being carried between the four helicopters. The helicopters dropped the object near the Angel and Misato finally noticed what it was. "Oh shit, that's a N-2 mine! Get down!" Misato yelled as she covered Naruto with her body. Naruto blushed as he felt her breast press into his face but got his hormones under control as he realized the danger they were both in. As the N-2 mine exploded, Naruto channeled his chakra into the wheels of the car to keep it from rolling due to the shock wave from the explosion. Misato got off of him when she felt the shock wave disperse. "Well, that was anti-climactic." Misato said with a sweatdrop.

It wasn't long after the N-2 mine that Misato and Naruto finally reached the elevator that took them down far below the surface until they reached a large door that had "NERV" on it. It separated and opened, allowing to continue down the road. Misato opened the passenger side opening under the dashboard and handed the two things in there to Naruto. "There is the manual about NERV and the device is where you put the ID you got in the letter and will act as your access to NERV and will allow you to access your funds for being employed here." Misato said as she continued driving. "Employed? The letter only said the Gendo wanted to see me?" Naruto said with an unnoticed tick on his head. 'He must really not get along with his father...can't say that I was any different with my father or that anyone really likes Commander Ikari.' Misato thought to herself.

A second door opened as they reached it and Naruto was surprised by what he saw. Below him was a green forest and above him were things that looked like buildings. "A geofront? I never thought that I would see one." Naruto said with a look of awe on his face. Misato smiled at him. "Yup, this is our secret base of operations, NERV HQ. This is the keystone for the resurrection of the world and the stronghold of humanity." Misato said as they finally reach the HQ.

After they finally reached the HQ, it seemed like they were walking for an hour. "Um Misato, are we lost?" he asked. "No no no, of course not. We're going the right way...I think." Misato says and Naruto sweatdrops.

They walked until a door behind them opened and a blonde woman in a lab coat walked out. "You're late Captain Katsuragi." Misato turned around. "Oh Ritsuko, s-sorry! I got lost...still don't have the layout of this place down yet!" Misato says with a laugh. Naruto stepped forward. "Its nice to meet you, I'm Naruto Ikari." he said with smile on his face. Ritsuko gave a slight smile. "I'm Ritsuko Akagi from the first engineering division...the supervisor of Project E." she said as she lead them the right way. They followed Ritsuko until they reached a boat in an unusual colored water. "Um...what is that?" Naruto asks pointing to the water or whatever it was. "That is LCL, you'll get used to it working here." Ritsuko explained as she started the boat.

As he listens to Ritsuko and Misato talk, he notices the dents in the walls and his eyes widen at the sight of a mechanical hand that had gone through the wall. 'What on earth has Gendo been working on here?' Naruto thought to himself as he saw several other heavy dents in the walls. They reached the dock for the boat and Ritsuko opened the door at the top of the stairs on the dock. "Be careful, it's dark so watch yourself." Ritsuko said as Naruto and Misato walked into the room.

Ritsuko pressed the light switch and Naruto was immediately face-to-face with a large, purple, robotic-looking head. "What...what is that thing?" Naruto asked. "She's a man-made, all purpose battle weapon. Artificial human Evangelion. This is humanity's last chance." Ritsuko explained. "So this is what Gendo has been working on?" Naruto asked as his hand moved across the metal. "That is correct." a voice came from an upper floor. Naruto turned to see Gendo looking down at him. "This is why I called you here, to pilot the Evangelion Unit 01. You're going to fight the Angel." Gendo said.

This was news to everyone in the room. "But Commander, it took Rei seven months to synchronize with the Eva, remember?! Naruto just got here and only just learned about the Eva, what you are asking is impossible!" Misato yelled. "There is no other choice, Katsuragi. He is the Third Child, one of the three capable of even moving the Evangelion. He has no option but to follow as he is told and pilot it." Gendo said with a condescending voice as he fixed his glasses.

Naruto stared Gendo down, focusing a bit of Killing Intent on his "father". "And why should I pilot it? I owe you nothing. You think that you can leave for eleven years and expect me to do as you say, to be follow an order that may cause my death? Screw you, you rotten bastard! I won't pilot it!" Naruto said defiantly. Gendo stared at Naruto before pressing a button on an intercom. "Fuyutsuki, the Third Child won't pilot it. Bring out Rei, she isn't dead yet." Gendo said without emotion.

Several doctors brought out a girl with light blue hair out on a gurney looking in bad condition. "Rei, the only replacement has refused to pilot. You must pilot it again." Gendo said as the girl attempted to sit up. "Yes, sir." she said, obviously in pain. 'Again? He already made her pilot earlier? Is that why she is so injured?!' Naruto thought as she fumed internally. "You monster. You think that you'll make me pilot by guilt tripping me?!" Naruto yells in rage. At that exact moment, the entire building shakes as the Angel attacks outside the geofront. "The city blocks on the ceiling of the dome are starting to fall!" Misato yelled. One of the light structures in the room fell from the ceiling onto the gurney that Rei was on, sending her to the floor. Naruto, using the reaction speed from his training, slid underneath Rei and prevented her from hitting the floor and held her in his arms. He looked at her as pain racked her body.

He got up and handed her to one of the doctors before turning back to Gendo. "Fine, I'll pilot it. I can't let others be hurt like she has." he said with determination in his voice. Ritsuko walked over to him. "Then come with me, I'll give you a simple lecture on the operating systems." she said as she lead him away. Gendo gave a smirk as Ritsuko led Naruto away. 'I knew that my plan would work. He always was too caring about others.' Gendo thought to himself as he went back to the bridge.

It wasn't very long before Naruto got into the pilot seat of the Entry plug and put on the A10 nerve clips (the things that go on the pilots' heads) as he gripped the controls. 'Okay, there is the release for the prog knife, the communication switch...' were Naruto's thoughts until LCL began to fill the entry plug. Ritsuko appeared on his screen. "Don't worry, Naruto. The LCL is oxygenated so you can breathe it in and get the oxygen to your bloodstream." Ritsuko explained as the Entry plug was inserted into the Evangelion.

Back on the bridge, Ritsuko walked over to a woman in her early twenties with dark brown hair and was wearing a normal NERV uniform. "What is his current synchronization rate, Maya?" Ritsuko asked. Maya typed into the terminal. "It can't be...it says he's already at 50% and climbing, senpai!" Maya said with awe. Ritsuko's eyes almost bulged as she saw the levels rise until they barely fluctuated between 64-68%. "Amazing. And this is just his first time in Unit 01." Ritsuko said with similar awe in her voice.

As Naruto sat waiting for what would happen next, he felt a small voice that seemed to whisper in his ear. He tried to listen to it but as soon as he thought he heard it, it disappeared. 'Things just keep getting weirder.' he thought to himself.

[On the bridge]

Ritsuko, Maya, and Misato were going over the final checks. "Syncho errors are within 0.3%." Maya said as she continued checking. "It's going to work." Ritsuko said to Misato who nodded. "Evangelion Unit-01! Prepare to launch!" Misato yelled. The restraints on the Eva started to released. "Transporting Eva Unit-01 to the launch elevator." Maya said as the restraints were all released. "Gate 5, standby. Launch path, clear. All green. Launch preparations are complete." Maya said and turned to Misato. "This is humanity's last chance. If we fail, there will be no future for humanity." Gendo said with his hands folded in front of his mouth. "Eva, launch!" Misato yelled and Unit-01 shot up the elevator.

To be continued...

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That's the end of the first chapter. Naruto has only seen everything up to his previous life in its entirety up to age ten. Things start to get more blurry and skip from that time on.

Ninpo: Henge (Transformation) - E rank - (hitsuji) - The user changes his/her appearance into something else using this jutsu.

Ninpo: Kage bushin (Shadow clone) - Kinjutsu, B rank - (cross seal) - Splits the user's chakra evenly to create a physical clone that can send by all information that it gains back to the user.

Ninpo: Chi bushin no jutsu (Blood clone) - Kinjutsu, A rank - (tora, tori, uma, u, tori, i, hitsuji) - Uses a small amount of blood to create a flesh and blood clone of the user that will last until it is killed or dispelled. Retains it knowledge like a **Kage bushin** but can last longer and the mental strain is less due to the information being more organized.


	2. Chapter 2

I have begun rewriting Ninja of Tokyo3 and have finished chapter 1. The rest of the story is still being rewritten and has changed drastically.


	3. Important AN

**Well I am sure many of you saw this coming. Ninja of Tokyo3 is officially discontinued. Now what you may not have expected: I am releasing a story to replace it. It is also a NarutoxNGE story but with a better plot, less plot hole, and less of a god mode Naruto. I have finished the first chapter and you should expect it to be on the site in a matter of hours if not right now. Go check out _A Second Age _and give me your thoughts on the improvements.**


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